Probe array data storage and retrieval

Abstract

Methods, systems and computer software products are provided for efficient management of large data sets. In one preferred embodiment, data are grouped according to their most frequent access requirement. Each group of the data is encoded as a single binary object. The binary objects are stored in a relational database. Component software product for encoding and decoding are also provided.

What is claimed is:  
     
         1 . A method for data storage comprising: 
 grouping a set of data according to its most common access requirements into a plurality of groups; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         2 . The method of  claim 1  wherein the database is a relational database.  
     
     
         3 . The method of  claim 2  wherein the set of data need not to be frequently accessed in arbitrary ways.  
     
     
         4 . The method of  claim 3  wherein the grouping comprises encoding the data into the binary objects by calling a component software.  
     
     
         5 . The method of  claim 3  wherein the component software is a COM object.  
     
     
         6 . The method of  claim 4  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         7 . The method of  claim 6  wherein the decoding comprises calling a component software for decoding.  
     
     
         8 . The method of  claim 7  wherein the component software is a COM object.  
     
     
         7 . The method of  claim 1  wherein the set of data is probe intensity data.  
     
     
         8 . The method of  claim 7  wherein the probe intensity data are from gene expression experiments and data from each probe set are grouped into one single binary object.  
     
     
         9 . The method of  claim 7  wherein the probe intensity data are grouped into a single binary object.  
     
     
         10 . The method of  claim 9  wherein at least 100 probe intensity values are grouped into a single binary object, wherein said 100 probe intensity values.  
     
     
         11 . The method of  claim 10  wherein at least 1000 probe intensity values are grouped into a single binary object.  
     
     
         12 . The method of  claim 1  wherein the set of data are probe design data comprising probe information.  
     
     
         13 . A method for managing probe array data, wherein the data comprising a plurality of intensity values for a plurality of probes, comprising: 
 grouping the intensity values into a plurality of groups according to most common access requirement; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         14 . The method of  claim 13  wherein the database is a relational database.  
     
     
         15 . The method of  claim 14  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         16 . The method of  claim 15  wherein each of the groups comprises at least 100 intensity values.  
     
     
         17 . The method of  claim 16  wherein each of the groups comprises at least 1000 intensity values.  
     
     
         18 . The method of  claim 17  wherein each of the groups comprises intensity values for a set of probes, wherein the set of probes is for detecting one transcript.  
     
     
         19 . The method of  claim 18  wherein the encoding comprises calling a component software.  
     
     
         20 . The method of  claim 18  wherein the component software is a COM object.  
     
     
         21 . The method of  claim 19  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         22 . A method for managing probe design information comprising: 
 grouping the probe design information into a plurality of groups according to the most common access requirement; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         23 . The method of  claim 22  wherein the database is a relational database.  
     
     
         24 . The method of  claim 23  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         25 . The method of  claim 24  wherein each of the groups comprises data for probes in a tiling segment.  
     
     
         26 . The method of  claim 25  wherein the segment is at least 25 bases.  
     
     
         27 . The method of  claim 26  wherein the segment is at least 250 bases.  
     
     
         28 . The method of  claim 28  wherein the encoding comprises calling a component software.  
     
     
         29 . The method of  claim 29  wherein the component software is a COM object.  
     
     
         30 . A system for data management comprising: 
 a processor; and    a memory coupled with the least one processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include: 
 grouping a set of data according to its most common access requirements into a plurality of groups; and  
 storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.  
   
     
     
         31 . The system of  claim 30  wherein the database is a relational database.  
     
     
         32 . The system of  claim 31  wherein the set of data need not to be frequently accessed in arbitrary ways.  
     
     
         33 . The system of  claim 32  wherein the grouping comprises encoding the data into the binary objects by calling a component software.  
     
     
         34 . The system of  claim 33  wherein the component software is a COM object.  
     
     
         35 . The system of  claim 34  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         36 . The system of  claim 35  wherein the decoding comprises calling a component software for decoding.  
     
     
         37 . The system of  claim 37  wherein the component software is a COM object.  
     
     
         38 . The system of  claim 30  wherein the set of data is probe intensity data.  
     
     
         39 . The system of  claim 38  wherein the probe intensity data are from gene expression experiments and data from each probe set are grouped into one single binary object.  
     
     
         40 . The system of  claim 39  wherein the probe intensity data are grouped into a single binary object.  
     
     
         41 . The system of  claim 40  wherein at least 100 probe intensity values are grouped into a single binary object.  
     
     
         42 . The system of  claim 41  wherein at least 1000 probe intensity values are grouped into a single binary object.  
     
     
         43 . The system of  claim 30  wherein the set of data are probe design data comprising probe information.  
     
     
         44 . A system for managing probe array data, wherein the data comprising a plurality of intensity values for a plurality of probes, comprising: 
 a processor; and    a memory coupled with the processor, the memory storing a plurality of machine instructions that cause the processor to perform logical steps, wherein the logical steps include: 
 grouping the intensity values into a plurality of groups according to the most common access requirement; and  
 storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.  
   
     
     
         45 . The system of  claim 44  wherein the database is a relational database.  
     
     
         46 . The system of  claim 45  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         47 . The system of  claim 46  wherein each of the groups comprises at least 100 intensity values.  
     
     
         48 . The system of  claim 47  wherein each of the groups comprises at least 1000 intensity values.  
     
     
         49 . The system of  claim 48  wherein each of the groups comprises intensity values for a set of probes, wherein the set of probes is for detecting one transcript.  
     
     
         50 . The system of  claim 49  wherein the encoding comprises calling a component software.  
     
     
         51 . The system of  claim 50  wherein the component software is a COM object.  
     
     
         52 . The system of  claim 51  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         53 . A system for managing probe array design data comprising: 
 a processor; and    a memory coupled with the processor, the memory storing a plurality machine instructions that cause the processor to perform logical steps, wherein the logical steps include: 
 grouping probe design information into a plurality of groups according to the most common access requirement; and  
 storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.  
   
     
     
         54 . The system of  claim 53  wherein the database is a relational database.  
     
     
         55 . The system of  claim 54  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         56 . The system of  claim 55  wherein each of the groups comprises data for probes in a tiling segment.  
     
     
         57 . The system of  claim 56  wherein the segment is at least 25 bases.  
     
     
         58 . The system of  claim 57  wherein the segment is at least 250 bases.  
     
     
         59 . The system of  claim 58  wherein the encoding comprises calling a component software.  
     
     
         60 . The system of  claim 59  wherein the component software is a COM object.  
     
     
         61 . The system of  claim 60  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         62 . The system of  claim 61  wherein the decoding comprises calling a component software for decoding.  
     
     
         63 . The system of  claim 62  wherein the component software is a COM object.  
     
     
         64 . A computer readable medium having stored thereon a data structure comprising: 
 a first table comprising a first field containing a first and a second field containing or referring to a binary object, wherein the binary object contains probe intensity values; and    a second table comprising a first field containing the first identifier, wherein the first table is related to second table by the first identifier.    
     
     
         65 . The computer readable medium of  claim 64  wherein the second table stores tiling design.  
     
     
         66 . A computer readable medium comprising computer-executable instructions for performing the methods comprising: 
 grouping a set of data according to its most common access requirements into a plurality of groups; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         67 . The computer readable medium of  claim 66  wherein the database is a relational database.  
     
     
         68 . The computer readable medium of  claim 67  wherein the set of data need not to be frequently accessed in arbitrary ways.  
     
     
         69 . The computer readable medium of  claim 68  wherein the grouping comprises encoding the data into the binary objects by calling a component software.  
     
     
         70 . The computer readable medium of  claim 69  wherein the component software is a COM object.  
     
     
         71 . The computer readable medium of  claim 68  further comprising; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         72 . The computer readable medium of  claim 71  wherein the decoding comprises calling a component software for decoding.  
     
     
         73 . The computer readable medium of  claim 72  wherein the component software is a COM object.  
     
     
         72 . The computer readable medium of  claim 66  wherein the set of data is probe intensity data.  
     
     
         73 . The computer readable medium of  claim 72  wherein the probe intensity data are from gene expression experiments and data from each probe set are grouped into one single binary object.  
     
     
         74 . The computer readable medium of  claim 73  wherein the probe intensity data are grouped into a single binary object.  
     
     
         75 . The computer readable medium of  claim 74  wherein at least 100 probe intensity values are grouped into a single binary object, wherein said 100 probe intensity values.  
     
     
         76 . The computer readable medium of  claim 75  wherein at least 1000 probe intensity values are grouped into a single binary object.  
     
     
         77 . The computer readable medium of  claim 66  wherein the set of data are probe design data comprising probe information.  
     
     
         78 . A computer readable medium for managing data, wherein the data comprising a plurality of intensity values for a plurality of probes, comprising computer-executable instructions for performing the method comprising: 
 grouping the intensity values into a plurality of groups according to most common access requirement; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         79 . The computer readable medium of  claim 78  wherein the database is a relational database.  
     
     
         80 . The computer readable medium of  claim 79  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         81 . The computer readable medium of  claim 80  wherein each of the groups comprises at least 100 intensity values.  
     
     
         82 . The computer readable medium of  claim 81  wherein each of the groups comprises at least 1000 intensity values.  
     
     
         83 . The computer readable medium of  claim 82  wherein each of the groups comprises intensity values for a set of probes, wherein the set of probes is for detecting one transcript.  
     
     
         84 . The computer readable medium of  claim 83  wherein the encoding comprises calling a component software.  
     
     
         85 . The computer readable medium of  claim 84  wherein the component software is a COM object.  
     
     
         86 . The computer readable medium of  claim 19  wherein the method further comprises; 
 retrieving the binary objects from the relational database;  
 decoding the binary objects into the set of data; wherein the binary objects are encoded in a data structure format that is compatible on a binary level with the decoding.  
 
     
     
         87 . A computer readable medium comprising computer-executable instructions for performing the methods comprising: 
 grouping the probe design information into a plurality of groups according to the most common access requirement; and    storing the groups in a database as single binary objects, wherein each of the groups is stored as one single binary object.    
     
     
         88 . The computer readable medium of  claim 88  wherein the database is a relational database.  
     
     
         89 . The computer readable medium of  claim 88  wherein the grouping comprises encoding the data into the binary objects.  
     
     
         90 . The computer readable medium of  claim 89  wherein each of the groups comprises data for probes in a tiling segment.  
     
     
         91 . The computer readable medium of claim  90  wherein the segment is at least 25 bases.  
     
     
         92 . The computer readable medium of claim  91  wherein the segment is at least 250 bases.  
     
     
         93 . The computer readable medium of claim  92  wherein the encoding comprises calling a component software.  
     
     
         94 . The computer readable medium of claim  93  wherein the component software is a COM object.